How To Remove Nonstandard Lines In Bed File

Question

[Phuong]

Hi

does anybody know how to remove lines that are not in the format

chr    5759    6184    ORF5759    1    -

I have bed file that contain

chr    5759    6184    ORF5759    1    -

sirna some number

How can remove all the lines that does not follow the format so I can upload file to ucsc. Thank you so much appreciate it

[Martin A Hansen]

This is not clear. What do the badly formatted lines look like? How did you come by this badly formatted BED file? What do you mean by "sirna some number"?

[Dataminer]

@phuong: could you be little descriptive in your question, it will help in answering it. SECONDLY, WHO SO EVER DOWN VOTED this question should have given a chance to phuong to ammend her question or a chance to describe it from a more clear perspective..... I am completely against of down voting questions... unless they are exact copies..

[brentp]

it appears that "sirna some number" is the bad line.

[Martin A Hansen]

Questions are down-voted when unclear or not useful - as it is explained in the mouse-over tooltip. This one was unclear. I am in fact helping out.

[Martin A Hansen]

If "sirna some number" is the problem you can remove those with grep -v "sirna".

Answer 1

[brentp]

If all you want is to remove lines that

1. Dont have at least 3 columns (BED must have at least Chr, start, end)
2. have integers in the 2nd and 3rd columns.

Then you can use this python script filter_bed.py):

import sys
for toks in (line.rstrip("\r\n").split("\t") for line in open(sys.argv[1])):
    if len(toks) < 3: continue
    if not (toks[1].isdigit() and toks[2].isdigit()): continue
    print "\t".join(toks)

Called like:

$ python filter_bed.py my.bad.bed > my.good.bed

UCSC may have other requirements, I can't recall, but this should give you a start.